{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:24:23Z","timestamp":1792790663519,"version":"4.5.0"},"reference-count":76,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2024,5,7]],"date-time":"2024-05-07T00:00:00Z","timestamp":1715040000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2024,5,7]],"date-time":"2024-05-07T00:00:00Z","timestamp":1715040000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100000051","name":"U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute","doi-asserted-by":"publisher","award":["R56HG012359"],"award-info":[{"award-number":["R56HG012359"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"},{"id":"https:\/\/ror.org\/00baak391","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000051","name":"U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute","doi-asserted-by":"publisher","award":["R01HG012359"],"award-info":[{"award-number":["R01HG012359"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"},{"id":"https:\/\/ror.org\/00baak391","id-type":"ROR","asserted-by":"crossref"}]},{"name":"U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute","id":[{"id":"https:\/\/ror.org\/00baak391","id-type":"ROR","asserted-by":"crossref"}]},{"DOI":"10.13039\/100000057","name":"U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R35GM145279"],"award-info":[{"award-number":["R35GM145279"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Nat Commun"],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>\n                    Pre-mRNA splicing, a key process in gene expression, can be therapeutically modulated using various drug modalities, including antisense oligonucleotides (ASOs). However, determining promising targets is hampered by the challenge of systematically mapping splicing-regulatory elements (SREs) in their native sequence context. Here, we use the catalytically inactive CRISPR-\n                    <jats:italic>Rfx<\/jats:italic>\n                    Cas13d RNA-targeting system (dCas13d\/gRNA) as a programmable platform to bind SREs and modulate splicing by competing against endogenous splicing factors. SpliceRUSH, a high-throughput screening method, was developed to map SREs in any gene of interest using a lentivirus gRNA library that tiles the genetic region, including distal intronic sequences. When applied to\n                    <jats:italic>SMN2<\/jats:italic>\n                    , a therapeutic target for spinal muscular atrophy, SpliceRUSH robustly identifies not only known SREs but also a previously unknown distal intronic SRE, which can be targeted to alter exon 7 splicing using either dCas13d\/gRNA or ASOs. This technology enables a deeper understanding of splicing regulation with applications for RNA-based drug discovery.\n                  <\/jats:p>","DOI":"10.1038\/s41467-024-47140-8","type":"journal-article","created":{"date-parts":[[2024,5,7]],"date-time":"2024-05-07T15:01:45Z","timestamp":1715094105000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":27,"title":["CRISPR-dCas13d-based deep screening of proximal and distal splicing-regulatory elements"],"prefix":"10.1038","volume":"15","author":[{"given":"Yocelyn","family":"Recinos","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmytro","family":"Ustianenko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yow-Tyng","family":"Yeh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojian","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Jacko","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lekha V.","family":"Yesantharao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiyang","family":"Wu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8310-7537","authenticated-orcid":false,"given":"Chaolin","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,5,7]]},"reference":[{"key":"47140_CR1","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1038\/271501a0","volume":"271","author":"W Gilbert","year":"1978","unstructured":"Gilbert, W. Why genes in pieces? Nature 271, 501 (1978).","journal-title":"Nature"},{"key":"47140_CR2","doi-asserted-by":"publisher","first-page":"3171","DOI":"10.1073\/pnas.74.8.3171","volume":"74","author":"SM Berget","year":"1977","unstructured":"Berget, S. M., Moore, C. & Sharp, P. A. Spliced segments at the 5\u2019 terminus of adenovirus 2 late mRNA. Proc. Natl Acad. Sci. USA 74, 3171\u20133175 (1977).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"47140_CR3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/0092-8674(77)90180-5","volume":"12","author":"LT Chow","year":"1977","unstructured":"Chow, L. T., Gelinas, R. E., Broker, T. R. & Roberts, R. J. An amazing sequence arrangement at the 5\u2019 ends of adenovirus 2 messenger RNA. Cell 12, 1\u20138 (1977).","journal-title":"Cell"},{"key":"47140_CR4","doi-asserted-by":"publisher","first-page":"1413","DOI":"10.1038\/ng.259","volume":"40","author":"Q Pan","year":"2008","unstructured":"Pan, Q., Shai, O., Lee, L. J., Frey, B. J. & Blencowe, B. J. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat. Genet. 40, 1413\u20131415 (2008).","journal-title":"Nat. Genet."},{"key":"47140_CR5","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1038\/nature07509","volume":"456","author":"ET Wang","year":"2008","unstructured":"Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470\u2013476 (2008).","journal-title":"Nature"},{"key":"47140_CR6","doi-asserted-by":"publisher","first-page":"457","DOI":"10.1038\/nature08909","volume":"463","author":"TW Nilsen","year":"2010","unstructured":"Nilsen, T. W. & Graveley, B. R. Expansion of the eukaryotic proteome by alternative splicing. Nature 463, 457\u2013463 (2010).","journal-title":"Nature"},{"key":"47140_CR7","doi-asserted-by":"publisher","first-page":"291","DOI":"10.1146\/annurev.biochem.72.121801.161720","volume":"72","author":"DL Black","year":"2003","unstructured":"Black, D. L. Mechanisms of alternative pre-messenger RNA splicing. Annu. Rev. Biochem. 72, 291\u2013336 (2003).","journal-title":"Annu. Rev. Biochem."},{"key":"47140_CR8","doi-asserted-by":"publisher","first-page":"75","DOI":"10.1038\/nrg2673","volume":"11","author":"DD Licatalosi","year":"2010","unstructured":"Licatalosi, D. D. & Darnell, R. B. RNA processing and its regulation: global insights into biological networks. Nat. Rev. Genet. 11, 75\u201387 (2010).","journal-title":"Nat. Rev. Genet."},{"key":"47140_CR9","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1016\/j.molcel.2019.09.017","volume":"76","author":"J Ule","year":"2019","unstructured":"Ule, J. & Blencowe, B. J. Alternative splicing regulatory networks: functions, mechanisms, and evolution. Mol. Cell 76, 329\u2013345 (2019).","journal-title":"Mol. Cell"},{"key":"47140_CR10","doi-asserted-by":"publisher","first-page":"777","DOI":"10.1016\/j.cell.2009.02.011","volume":"136","author":"TA Cooper","year":"2009","unstructured":"Cooper, T. A., Wan, L. & Dreyfuss, G. RNA and disease. Cell 136, 777\u2013793 (2009).","journal-title":"Cell"},{"key":"47140_CR11","doi-asserted-by":"publisher","first-page":"11093","DOI":"10.1073\/pnas.1101135108","volume":"108","author":"KH Lim","year":"2011","unstructured":"Lim, K. H., Ferraris, L., Filloux, M. E., Raphael, B. J. & Fairbrother, W. G. Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc. Natl Acad. Sci. USA 108, 11093\u201311098 (2011).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"47140_CR12","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1038\/nature13908","volume":"515","author":"I Iossifov","year":"2014","unstructured":"Iossifov, I. et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature 515, 216\u2013221 (2014).","journal-title":"Nature"},{"key":"47140_CR13","doi-asserted-by":"publisher","first-page":"673","DOI":"10.1038\/s41573-020-0075-7","volume":"19","author":"TC Roberts","year":"2020","unstructured":"Roberts, T. C., Langer, R. & Wood, M. J. A. Advances in oligonucleotide drug delivery. Nat. Rev. Drug Discov. 19, 673\u2013694 (2020).","journal-title":"Nat. Rev. Drug Discov."},{"key":"47140_CR14","doi-asserted-by":"publisher","first-page":"2004","DOI":"10.3390\/jcm9062004","volume":"9","author":"K Dhuri","year":"2020","unstructured":"Dhuri, K. et al. Antisense oligonucleotides: an emerging area in drug discovery and development. J. Clin. Med. 9, 2004 (2020).","journal-title":"J. Clin. Med."},{"key":"47140_CR15","doi-asserted-by":"publisher","first-page":"232","DOI":"10.31662\/jmaj.2021-0019","volume":"4","author":"M Matsuo","year":"2021","unstructured":"Matsuo, M. Antisense oligonucleotide-mediated exon-skipping therapies: precision medicine spreading from Duchenne muscular dystrophy. JMA J. 4, 232\u2013240 (2021).","journal-title":"JMA J."},{"key":"47140_CR16","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.aaz6100","volume":"12","author":"Z Han","year":"2020","unstructured":"Han, Z. et al. Antisense oligonucleotides increase Scn1a expression and reduce seizures and SUDEP incidence in a mouse model of Dravet syndrome. Sci. Transl. Med. 12, eaaz6100 (2020).","journal-title":"Sci. Transl. Med."},{"key":"47140_CR17","doi-asserted-by":"publisher","first-page":"7","DOI":"10.4161\/rna.4.1.4535","volume":"4","author":"RN Singh","year":"2007","unstructured":"Singh, R. N. Evolving concepts on human SMN pre-mRNA splicing. RNA Biol. 4, 7\u201310 (2007).","journal-title":"RNA Biol."},{"key":"47140_CR18","doi-asserted-by":"publisher","first-page":"100416","DOI":"10.1016\/j.jbc.2021.100416","volume":"296","author":"ST Crooke","year":"2021","unstructured":"Crooke, S. T., Liang, X. H., Baker, B. F. & Crooke, R. M. Antisense technology: A review. J. Biol. Chem. 296, 100416 (2021).","journal-title":"J. Biol. Chem."},{"key":"47140_CR19","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1261\/rna.876308","volume":"14","author":"Z Wang","year":"2008","unstructured":"Wang, Z. & Burge, C. B. Splicing regulation: from a parts list of regulatory elements to an integrated splicing code. RNA 14, 802\u2013813 (2008).","journal-title":"RNA"},{"key":"47140_CR20","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-018-1437-x","volume":"19","author":"SI Adamson","year":"2018","unstructured":"Adamson, S. I., Zhan, L. & Graveley, B. R. Vex-seq: high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency. Genome Biol. 19, 71 (2018).","journal-title":"Genome Biol."},{"key":"47140_CR21","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1016\/j.molcel.2018.10.037","volume":"73","author":"R Cheung","year":"2019","unstructured":"Cheung, R. et al. A multiplexed assay for exon recognition reveals that an unappreciated fraction of rare genetic variants cause large-effect splicing disruptions. Mol. Cell 73, 183\u2013194.e188 (2019).","journal-title":"Mol. Cell"},{"key":"47140_CR22","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1038\/ng.3837","volume":"49","author":"R Soemedi","year":"2017","unstructured":"Soemedi, R. et al. Pathogenic variants that alter protein code often disrupt splicing. Nat. Genet. 49, 848\u2013855 (2017).","journal-title":"Nat. Genet."},{"key":"47140_CR23","doi-asserted-by":"publisher","first-page":"831","DOI":"10.1016\/j.cell.2004.11.010","volume":"119","author":"ZF Wang","year":"2004","unstructured":"Wang, Z. F. et al. Systematic identification and analysis of exonic splicing silencers. Cell 119, 831\u2013845 (2004).","journal-title":"Cell"},{"key":"47140_CR24","doi-asserted-by":"publisher","first-page":"1224","DOI":"10.1016\/j.cell.2008.10.046","volume":"135","author":"Y Yu","year":"2008","unstructured":"Yu, Y. et al. Dynamic regulation of alternative splicing by silencers that modulate 5\u2019 splice site competition. Cell 135, 1224\u20131236 (2008).","journal-title":"Cell"},{"key":"47140_CR25","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1126\/science.1073774","volume":"297","author":"WG Fairbrother","year":"2002","unstructured":"Fairbrother, W. G., Yeh, R.-F., Sharp, P. A. & Burge, C. B. Predictive identification of exonic splicing enhancers in human genes. Science 297, 1007\u20131013 (2002).","journal-title":"Science"},{"key":"47140_CR26","doi-asserted-by":"publisher","first-page":"1241","DOI":"10.1101\/gad.1195304","volume":"18","author":"XH-F Zhang","year":"2004","unstructured":"Zhang, X. H.-F. & Chasin, L. A. Computational definition of sequence motifs governing constitutive exon splicing. Genes Dev. 18, 1241\u20131250 (2004).","journal-title":"Genes Dev."},{"key":"47140_CR27","doi-asserted-by":"publisher","first-page":"769","DOI":"10.1016\/j.molcel.2006.05.008","volume":"22","author":"A Goren","year":"2006","unstructured":"Goren, A. et al. Comparative analysis identifies exonic splicing regulatory sequences-the complex definition of enhancers and silencers. Mol. Cell 22, 769\u2013781 (2006).","journal-title":"Mol. Cell"},{"key":"47140_CR28","doi-asserted-by":"publisher","first-page":"698","DOI":"10.1016\/j.cell.2015.09.054","volume":"163","author":"AB Rosenberg","year":"2015","unstructured":"Rosenberg, A. B., Patwardhan, R. P., Shendure, J. & Seelig, G. Learning the sequence determinants of alternative splicing from millions of random sequences. Cell 163, 698\u2013711 (2015).","journal-title":"Cell"},{"key":"47140_CR29","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1038\/nature09000","volume":"465","author":"Y Barash","year":"2010","unstructured":"Barash, Y. et al. Deciphering the splicing code. Nature 465, 53\u201359 (2010).","journal-title":"Nature"},{"key":"47140_CR30","doi-asserted-by":"publisher","first-page":"1254806","DOI":"10.1126\/science.1254806","volume":"347","author":"HY Xiong","year":"2015","unstructured":"Xiong, H. Y. et al. The human splicing code reveals new insights into the genetic determinants of disease. Science 347, 1254806 (2015).","journal-title":"Science"},{"key":"47140_CR31","doi-asserted-by":"publisher","first-page":"5797","DOI":"10.1073\/pnas.0801692105","volume":"105","author":"C Zhang","year":"2008","unstructured":"Zhang, C., Li, W.-H., Krainer, A. R. & Zhang, M. Q. RNA landscape of evolution for optimal exon and intron discrimination. Proc. Natl Acad. Sci. USA 105, 5797\u20135802 (2008).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"47140_CR32","doi-asserted-by":"publisher","first-page":"33641","DOI":"10.1074\/jbc.M005597200","volume":"275","author":"N Guo","year":"2000","unstructured":"Guo, N. & Kawamoto, S. An intronic downstream enhancer promotes 3\u2019 splice site usage of a neural cell-specific exon. J. Biol. Chem. 275, 33641\u201333649 (2000).","journal-title":"J. Biol. Chem."},{"key":"47140_CR33","doi-asserted-by":"publisher","first-page":"1434","DOI":"10.1038\/nsmb.2699","volume":"20","author":"MT Lovci","year":"2013","unstructured":"Lovci, M. T. et al. Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat. Struct. Mol. Biol. 20, 1434\u20131442 (2013).","journal-title":"Nat. Struct. Mol. Biol."},{"key":"47140_CR34","doi-asserted-by":"publisher","first-page":"aaf5573","DOI":"10.1126\/science.aaf5573","volume":"353","author":"OO Abudayyeh","year":"2016","unstructured":"Abudayyeh, O. O. et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353, aaf5573 (2016).","journal-title":"Science"},{"key":"47140_CR35","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1016\/j.molcel.2017.04.008","volume":"66","author":"A East-Seletsky","year":"2017","unstructured":"East-Seletsky, A., O\u2019Connell, M. R., Burstein, D., Knott, G. J. & Doudna, J. A. RNA targeting by functionally orthogonal type VI-A CRISPR-Cas enzymes. Mol. Cell 66, 373\u2013383.e373 (2017).","journal-title":"Mol. Cell"},{"key":"47140_CR36","doi-asserted-by":"publisher","first-page":"618","DOI":"10.1016\/j.molcel.2016.12.023","volume":"65","author":"AA Smargon","year":"2017","unstructured":"Smargon, A. A. et al. Cas13b is a type VI-B CRISPR-associated RNA-guided RNase differentially regulated by accessory proteins Csx27 and Csx28. Mol. Cell 65, 618\u2013630.e617 (2017).","journal-title":"Mol. Cell"},{"key":"47140_CR37","doi-asserted-by":"publisher","first-page":"665","DOI":"10.1016\/j.cell.2018.02.033","volume":"173","author":"S Konermann","year":"2018","unstructured":"Konermann, S. et al. Transcriptome engineering with RNA-targeting type VI-D CRISPR effectors. Cell 173, 665\u2013676.e614 (2018).","journal-title":"Cell"},{"key":"47140_CR38","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1016\/j.molcel.2018.02.028","volume":"70","author":"WX Yan","year":"2018","unstructured":"Yan, W. X. et al. Cas13d Is a compact RNA-targeting type VI CRISPR effector positively modulated by a WYL-domain-containing accessory protein. Mol. Cell 70, 327\u2013339 (2018).","journal-title":"Mol. Cell"},{"key":"47140_CR39","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/j.molcel.2015.10.008","volume":"60","author":"S Shmakov","year":"2015","unstructured":"Shmakov, S. et al. Discovery and functional characterization of diverse class 2 CRISPR-Cas systems. Mol. Cell 60, 385\u2013397 (2015).","journal-title":"Mol. Cell"},{"key":"47140_CR40","doi-asserted-by":"publisher","first-page":"499","DOI":"10.1038\/s41592-021-01124-4","volume":"18","author":"C Xu","year":"2021","unstructured":"Xu, C. et al. Programmable RNA editing with compact CRISPR-Cas13 systems from uncultivated microbes. Nat. Methods 18, 499\u2013506 (2021).","journal-title":"Nat. Methods"},{"key":"47140_CR41","doi-asserted-by":"crossref","unstructured":"Wei, J. et al. Deep learning and CRISPR-Cas13d ortholog discovery for optimized RNA targeting. Cell Syst. 14, 1087\u20131102.e1013 (2023).","DOI":"10.1016\/j.cels.2023.11.006"},{"key":"47140_CR42","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1038\/s41587-020-0456-9","volume":"38","author":"H-H Wessels","year":"2020","unstructured":"Wessels, H.-H. et al. Massively parallel Cas13 screens reveal principles for guide RNA design. Nat. Biotech. 38, 722\u2013727 (2020).","journal-title":"Nat. Biotech."},{"key":"47140_CR43","doi-asserted-by":"crossref","unstructured":"Li, Z. et al. Intrinsic targeting of host RNA by Cas13 constrains its utility. Nat. Biomed. Eng. 8, 177\u2013192 (2024).","DOI":"10.1038\/s41551-023-01109-y"},{"key":"47140_CR44","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-021-02263-9","volume":"22","author":"Y Zhang","year":"2021","unstructured":"Zhang, Y. et al. Optimized RNA-targeting CRISPR\/Cas13d technology outperforms shRNA in identifying functional circRNAs. Genome Biol. 22, 41 (2021).","journal-title":"Genome Biol."},{"key":"47140_CR45","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-023-36316-3","volume":"14","author":"X Cheng","year":"2023","unstructured":"Cheng, X. et al. Modeling CRISPR-Cas13d on-target and off-target effects using machine learning approaches. Nat. Commun. 14, 752 (2023).","journal-title":"Nat. Commun."},{"key":"47140_CR46","doi-asserted-by":"publisher","first-page":"51","DOI":"10.1038\/s41592-020-01011-4","volume":"18","author":"SQ Li","year":"2021","unstructured":"Li, S. Q. et al. Screening for functional circular RNAs using the CRISPR-Cas13 system. Nat. Methods 18, 51\u201359 (2021).","journal-title":"Nat. Methods"},{"key":"47140_CR47","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-020-58104-5","volume":"10","author":"D Xu","year":"2020","unstructured":"Xu, D. et al. A CRISPR\/Cas13-based approach demonstrates biological relevance of vlinc class of long non-coding RNAs in anticancer drug response. Sci. Rep. 10, 1794 (2020).","journal-title":"Sci. Rep."},{"key":"47140_CR48","doi-asserted-by":"publisher","first-page":"1019","DOI":"10.1126\/science.aaq0180","volume":"358","author":"DBT Cox","year":"2017","unstructured":"Cox, D. B. T. et al. RNA editing with CRISPR-Cas13. Science 358, 1019\u20131027 (2017).","journal-title":"Science"},{"key":"47140_CR49","doi-asserted-by":"publisher","first-page":"1431","DOI":"10.1038\/s41587-020-0572-6","volume":"38","author":"C Wilson","year":"2020","unstructured":"Wilson, C., Chen, P. J., Miao, Z. & Liu, D. R. Programmable m(6)A modification of cellular RNAs with a Cas13-directed methyltransferase. Nat. Biotechnol. 38, 1431\u20131440 (2020).","journal-title":"Nat. Biotechnol."},{"key":"47140_CR50","doi-asserted-by":"publisher","first-page":"648","DOI":"10.1016\/j.molcel.2020.10.019","volume":"80","author":"NK Leclair","year":"2020","unstructured":"Leclair, N. K. et al. Poison exon splicing regulates a coordinated network of SR protein expression during differentiation and tumorigenesis. Mol. Cell 80, 648\u2013665.e649 (2020).","journal-title":"Mol. Cell"},{"key":"47140_CR51","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-020-16806-4","volume":"11","author":"M Du","year":"2020","unstructured":"Du, M., Jillette, N., Zhu, J. J., Li, S. & Cheng, A. W. CRISPR artificial splicing factors. Nat. Commun. 11, 2973 (2020).","journal-title":"Nat. Commun."},{"key":"47140_CR52","doi-asserted-by":"crossref","unstructured":"Anderson, K.M., Poosala, P., Lindley, S.R. & Anderson, D.M. Targeted cleavage and polyadenylation of RNA by CRISPR-Cas13. Preprint at https:\/\/www.biorxiv.org\/content\/10.1101\/531111v1 (2019).","DOI":"10.1101\/531111"},{"key":"47140_CR53","doi-asserted-by":"publisher","first-page":"280","DOI":"10.1038\/nature24049","volume":"550","author":"OO Abudayyeh","year":"2017","unstructured":"Abudayyeh, O. O. et al. RNA targeting with CRISPR-Cas13. Nature 550, 280\u2013284 (2017).","journal-title":"Nature"},{"key":"47140_CR54","doi-asserted-by":"publisher","first-page":"22068","DOI":"10.1073\/pnas.2006617117","volume":"117","author":"S Han","year":"2020","unstructured":"Han, S. et al. RNA-protein interaction mapping via MS2- or Cas13-based APEX targeting. Proc. Natl Acad. Sci. USA 117, 22068\u201322079 (2020).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"47140_CR55","doi-asserted-by":"crossref","unstructured":"Charles, E.J. et al. Engineering improved Cas13 effectors for targeted post-transcriptional regulation of gene expression. Preprint at https:\/\/www.biorxiv.org\/content\/10.1101\/2021.05.26.445687v1.full (2021).","DOI":"10.1101\/2021.05.26.445687"},{"key":"47140_CR56","doi-asserted-by":"publisher","first-page":"435","DOI":"10.1111\/ahg.12031","volume":"77","author":"DK Nurputra","year":"2013","unstructured":"Nurputra, D. K. et al. Spinal muscular atrophy: from gene discovery to clinical trials. Ann. Hum. Genet 77, 435\u2013463 (2013).","journal-title":"Ann. Hum. Genet"},{"key":"47140_CR57","doi-asserted-by":"publisher","first-page":"6307","DOI":"10.1073\/pnas.96.11.6307","volume":"96","author":"CL Lorson","year":"1999","unstructured":"Lorson, C. L., Hahnen, E., Androphy, E. J. & Wirth, B. A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy. Proc. Natl Acad. Sci. USA 96, 6307\u20136311 (1999).","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"47140_CR58","doi-asserted-by":"publisher","first-page":"1333","DOI":"10.1128\/MCB.26.4.1333-1346.2006","volume":"26","author":"NK Singh","year":"2006","unstructured":"Singh, N. K., Singh, N. N., Androphy, E. J. & Singh, R. N. Splicing of a critical exon of human survival motor neuron is regulated by a unique silencer element located in the last intron. Mol. Cell Biol. 26, 1333\u20131346 (2006).","journal-title":"Mol. Cell Biol."},{"key":"47140_CR59","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1038\/gt.2017.34","volume":"24","author":"NN Singh","year":"2017","unstructured":"Singh, N. N., Howell, M. D., Androphy, E. J. & Singh, R. N. How the discovery of ISS-N1 led to the first medical therapy for spinal muscular atrophy. Gene Ther. 24, 520\u2013526 (2017).","journal-title":"Gene Ther."},{"key":"47140_CR60","doi-asserted-by":"publisher","first-page":"1634","DOI":"10.1101\/gad.1941310","volume":"24","author":"Y Hua","year":"2010","unstructured":"Hua, Y. et al. Antisense correction of SMN2 splicing in the CNS rescues necrosis in a type III SMA mouse model. Genes Dev. 24, 1634\u20131644 (2010).","journal-title":"Genes Dev."},{"key":"47140_CR61","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1038\/nature10485","volume":"478","author":"Y Hua","year":"2011","unstructured":"Hua, Y. et al. Peripheral SMN restoration is essential for long-term rescue of a severe spinal muscular atrophy mouse model. Nature 478, 123\u2013126 (2011).","journal-title":"Nature"},{"key":"47140_CR62","doi-asserted-by":"publisher","first-page":"e73","DOI":"10.1371\/journal.pbio.0050073","volume":"5","author":"Y Hua","year":"2007","unstructured":"Hua, Y., Vickers, T. A., Baker, B. F., Bennett, C. F. & Krainer, A. R. Enhancement of SMN2 exon 7 inclusion by antisense oligonucleotides targeting the exon. PLoS Biol. 5, e73 (2007).","journal-title":"PLoS Biol."},{"key":"47140_CR63","doi-asserted-by":"publisher","first-page":"834","DOI":"10.1016\/j.ajhg.2008.01.014","volume":"82","author":"Y Hua","year":"2008","unstructured":"Hua, Y., Vickers, T. A., Okunola, H. L., Bennett, C. F. & Krainer, A. R. Antisense masking of an hnRNP A1\/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice. Am. J. Hum. Genet. 82, 834\u2013848 (2008).","journal-title":"Am. J. Hum. Genet."},{"key":"47140_CR64","doi-asserted-by":"publisher","first-page":"e148","DOI":"10.1093\/nar\/gkl967","volume":"34","author":"JP Orengo","year":"2006","unstructured":"Orengo, J. P., Bundman, D. & Cooper, T. A. A bichromatic fluorescent reporter for cell-based screens of alternative splicing. Nucleic Acids Res. 34, e148 (2006).","journal-title":"Nucleic Acids Res."},{"key":"47140_CR65","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1038\/nmeth944","volume":"3","author":"H Kuroyanagi","year":"2006","unstructured":"Kuroyanagi, H., Kobayashi, T., Mitani, S. & Hagiwara, M. Transgenic alternative-splicing reporters reveal tissue-specific expression profiles and regulation mechanisms in vivo. Nat. Meth 3, 909\u2013915 (2006).","journal-title":"Nat. Meth"},{"key":"47140_CR66","doi-asserted-by":"publisher","first-page":"998","DOI":"10.1101\/gr.147546.112","volume":"23","author":"S Zheng","year":"2013","unstructured":"Zheng, S., Damoiseaux, R., Chen, L. & Black, D. L. A broadly applicable high-throughput screening strategy identifies new regulators of Dlg4 (Psd-95) alternative splicing. Genome Res. 23, 998\u20131007 (2013).","journal-title":"Genome Res."},{"key":"47140_CR67","doi-asserted-by":"publisher","first-page":"259","DOI":"10.1093\/hmg\/9.2.259","volume":"9","author":"CL Lorson","year":"2000","unstructured":"Lorson, C. L. & Androphy, E. J. An exonic enhancer is required for inclusion of an essential exon in the SMA-determining gene SMN. Hum. Mol. Genet. 9, 259\u2013265 (2000).","journal-title":"Hum. Mol. Genet."},{"key":"47140_CR68","doi-asserted-by":"publisher","first-page":"9618","DOI":"10.1073\/pnas.160181697","volume":"97","author":"Y Hofmann","year":"2000","unstructured":"Hofmann, Y., Lorson, C. L., Stamm, S., Androphy, E. J. & Wirth, B. Htra2-beta 1 stimulates an exonic splicing enhancer and can restore full-length SMN expression to survival motor neuron 2 (SMN2). PNAS 97, 9618\u20139623 (2000).","journal-title":"PNAS"},{"key":"47140_CR69","doi-asserted-by":"crossref","unstructured":"N\u00fa\u00f1ez-\u00c1lvarez, Y., Espie-Caullet, T. & Luco, R.F. A CRISPR-dCas13 RNA-editing tool to study alternative splicing. Preprint at https:\/\/www.biorxiv.org\/content\/10.1101\/2022.05.24.493209v1 (2022).","DOI":"10.1101\/2022.05.24.493209"},{"key":"47140_CR70","doi-asserted-by":"publisher","first-page":"266","DOI":"10.1002\/wrna.31","volume":"1","author":"RB Darnell","year":"2010","unstructured":"Darnell, R. B. HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip. Rev. RNA 1, 266\u2013286 (2010).","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"47140_CR71","doi-asserted-by":"publisher","first-page":"354","DOI":"10.1016\/j.molcel.2018.01.005","volume":"69","author":"FCY Lee","year":"2018","unstructured":"Lee, F. C. Y. & Ule, J. Advances in CLIP technologies for studies of protein-RNA Interactions. Mol. Cell 69, 354\u2013369 (2018).","journal-title":"Mol. Cell"},{"key":"47140_CR72","doi-asserted-by":"publisher","first-page":"711","DOI":"10.1038\/s41586-020-2077-3","volume":"583","author":"EL Van Nostrand","year":"2020","unstructured":"Van Nostrand, E. L. et al. A large-scale binding and functional map of human RNA-binding proteins. Nature 583, 711\u2013719 (2020).","journal-title":"Nature"},{"key":"47140_CR73","doi-asserted-by":"publisher","first-page":"828","DOI":"10.1038\/nprot.2017.016","volume":"12","author":"J Joung","year":"2017","unstructured":"Joung, J. et al. Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. Nat. Protoc. 12, 828\u2013863 (2017).","journal-title":"Nat. Protoc."},{"key":"47140_CR74","doi-asserted-by":"publisher","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. Roy. Stat. Soc. B 57, 289\u2013300 (1995).","journal-title":"J. Roy. Stat. Soc. B"},{"key":"47140_CR75","doi-asserted-by":"publisher","first-page":"5149","DOI":"10.1093\/nar\/gkt216","volume":"41","author":"J Wu","year":"2013","unstructured":"Wu, J., Anczukow, O., Krainer, A. R., Zhang, M. Q. & Zhang, C. OLego: Fast and sensitive mapping of spliced mRNA-Seq reads using small seeds. Nucleic Acids Res 41, 5149\u20135163 (2013).","journal-title":"Nucleic Acids Res"},{"key":"47140_CR76","doi-asserted-by":"publisher","first-page":"3445","DOI":"10.1073\/pnas.1502849112","volume":"112","author":"Q Yan","year":"2015","unstructured":"Yan, Q. et al. Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators. Proc. Natl Acad. Sci. USA 112, 3445\u20133350 (2015).","journal-title":"Proc. Natl Acad. Sci. USA"}],"container-title":["Nature Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-47140-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-47140-8","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-47140-8.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,5,7]],"date-time":"2024-05-07T16:13:05Z","timestamp":1715098385000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/s41467-024-47140-8"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,5,7]]},"references-count":76,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,12]]}},"alternative-id":["47140"],"URL":"https:\/\/doi.org\/10.1038\/s41467-024-47140-8","relation":{},"ISSN":["2041-1723"],"issn-type":[{"value":"2041-1723","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,5,7]]},"assertion":[{"value":"21 June 2023","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 March 2024","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"7 May 2024","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Y.R., D.U., and C.Z. are inventors on a patent application submitted based on this work. C.Z. is a co-founder of DAYI Therapeutics, Inc. The other authors declare no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"3839"}}